Lincoln D. Stein > Bio-Graphics-2.12

Bio-Graphics-2.12

This Release Bio-Graphics-2.12  [Download] [Browse 31 Aug 2010
Latest Release Bio-Graphics-2.38  [Download] [Browse 23 Jul 2014
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License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
Build.PL
Changes
Makefile.PL
MANIFEST
META.yml
README

Modules

Bio::Graphics Generate GD images of Bio::Seq objects     2.12
Bio::Graphics::ConfiguratorI A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag->value semantics (ie. of Bio::AnnotationCollectionI) for object-representation inform     
Bio::Graphics::DrawTransmembrane draw a cartoon of an Alpha-helical transmembrane protein.      
Bio::Graphics::Feature A simple feature object for use with Bio::Graphics::Panel      
Bio::Graphics::FeatureBase Compatibility module      
Bio::Graphics::FeatureDir A directory of feature files and conf files      
Bio::Graphics::FeatureFile A set of Bio::Graphics features, stored in a file      
Bio::Graphics::FeatureFile::Iterator Iterator across a Bio::Graphics::FeatureFile      
Bio::Graphics::FileSplitter      
Bio::Graphics::Glyph Base class for Bio::Graphics::Glyph objects      
Bio::Graphics::Glyph::Factory Factory for Bio::Graphics::Glyph objects      
Bio::Graphics::Glyph::alignment The "alignment" glyph      
Bio::Graphics::Glyph::allele_tower The "allele_tower" glyph      
Bio::Graphics::Glyph::anchored_arrow The "anchored_arrow" glyph      
Bio::Graphics::Glyph::arrow the "arrow" glyph      
Bio::Graphics::Glyph::box The "box" glyph      
Bio::Graphics::Glyph::broken_line The "broken line" glyph      
Bio::Graphics::Glyph::cds The "cds" glyph      
Bio::Graphics::Glyph::christmas_arrow The "christmas arrow" glyph      
Bio::Graphics::Glyph::cross      
Bio::Graphics::Glyph::crossbox The "crossbox" glyph      
Bio::Graphics::Glyph::dashed_line The "dashed line" glyph      
Bio::Graphics::Glyph::diamond The "diamond" glyph      
Bio::Graphics::Glyph::dna The "dna" glyph      
Bio::Graphics::Glyph::dot The "dot" glyph      
Bio::Graphics::Glyph::dumbbell A glyph that draws a "dumbbell" with the same shapes on both ends.      
Bio::Graphics::Glyph::ellipse The "ellipse" glyph      
Bio::Graphics::Glyph::ex the "ex", or "crossed box" glyph      
Bio::Graphics::Glyph::extending_arrow The "extending arrow" glyph      
Bio::Graphics::Glyph::fixedwidth A base class fixed width glyphs      
Bio::Graphics::Glyph::flag the "flag" glyph      
Bio::Graphics::Glyph::gene A GFF3-compatible gene glyph      
Bio::Graphics::Glyph::generic The "generic" glyph      
Bio::Graphics::Glyph::graded_segments The "graded_segments" glyph      
Bio::Graphics::Glyph::group The "group" glyph      
Bio::Graphics::Glyph::hat The "hat" glyph      
Bio::Graphics::Glyph::heat_map The "heat_map" glyph      
Bio::Graphics::Glyph::heat_map_ideogram The "heat_map_ideogram" glyph      
Bio::Graphics::Glyph::heterogeneous_segments The "heterogeneous_segments" glyph      
Bio::Graphics::Glyph::hidden The "hidden" glyph      
Bio::Graphics::Glyph::hybrid_plot An xyplot plot drawing dual graph using data from two wiggle files per track     1.0
Bio::Graphics::Glyph::ideogram The "ideogram" glyph      
Bio::Graphics::Glyph::image A glyph that draws photographs & other images      
Bio::Graphics::Glyph::lightning The "lightning" glyph      
Bio::Graphics::Glyph::line The "line" glyph      
Bio::Graphics::Glyph::merge_parts a base class which suppors semantic zooming of scored alignment features      
Bio::Graphics::Glyph::merged_alignment The "merged_alignment" glyph      
Bio::Graphics::Glyph::minmax The minmax glyph      
Bio::Graphics::Glyph::oval The "oval" glyph      
Bio::Graphics::Glyph::pairplot The "pairwise plot" glyph      
Bio::Graphics::Glyph::pentagram The "pentagram" glyph      
Bio::Graphics::Glyph::phylo_align The "phylogenetic alignment" glyph      
Bio::Graphics::Glyph::pinsertion The "Drosophila P-element Insertion" glyph      
Bio::Graphics::Glyph::primers The "STS primers" glyph      
Bio::Graphics::Glyph::processed_transcript The sequence ontology transcript glyph      
Bio::Graphics::Glyph::protein The "protein" glyph      
Bio::Graphics::Glyph::ragged_ends The "ragged ends" glyph      
Bio::Graphics::Glyph::rainbow_gene A GFF3-compatible gene glyph      
Bio::Graphics::Glyph::redgreen_box The "redgreen_box" glyph      
Bio::Graphics::Glyph::redgreen_segment The "redgreen_segments" glyph      
Bio::Graphics::Glyph::repeating_shape A glyph that draws the same shape repeatedly.      
Bio::Graphics::Glyph::rndrect The "round rect" glyph      
Bio::Graphics::Glyph::ruler_arrow glyph for drawing an arrow as ruler (5' and 3' are marked as label)      
Bio::Graphics::Glyph::saw_teeth The "saw teeth" glyph      
Bio::Graphics::Glyph::segmented_keyglyph The "segmented_keyglyph" glyph      
Bio::Graphics::Glyph::segments The "segments" glyph      
Bio::Graphics::Glyph::smoothing      
Bio::Graphics::Glyph::so_transcript The sequence ontology transcript glyph      
Bio::Graphics::Glyph::span The "span" glyph      
Bio::Graphics::Glyph::spectrogram The "spectrogram" glyph      
Bio::Graphics::Glyph::splice_site The "splice_site" glyph      
Bio::Graphics::Glyph::stackedplot The stackedplot glyph      
Bio::Graphics::Glyph::ternary_plot Draw ternary plot data      
Bio::Graphics::Glyph::text_in_box The "text in box" glyph      
Bio::Graphics::Glyph::three_letters DAS-compatible package to use for drawing a line of groups of three letters      
Bio::Graphics::Glyph::tic_tac_toe The "tic-tac-toe" glyph      
Bio::Graphics::Glyph::toomany The "too many to show" glyph      
Bio::Graphics::Glyph::trace A glyph that visualizes a trace file      
Bio::Graphics::Glyph::track The "track" glyph      
Bio::Graphics::Glyph::transcript The "transcript" glyph      
Bio::Graphics::Glyph::transcript2 The "transcript2" glyph      
Bio::Graphics::Glyph::translation The "6-frame translation" glyph      
Bio::Graphics::Glyph::triangle The "triangle" glyph      
Bio::Graphics::Glyph::two_bolts The "two bolts" glyph      
Bio::Graphics::Glyph::wave The "wave" glyph      
Bio::Graphics::Glyph::weighted_arrow The "weighted arrow" glyph      
Bio::Graphics::Glyph::whiskerplot The whiskerplot glyph      
Bio::Graphics::Glyph::wiggle_box A generic box glyph compatible with dense "wig"data      
Bio::Graphics::Glyph::wiggle_density A density plot compatible with dense "wig"data      
Bio::Graphics::Glyph::wiggle_minmax      
Bio::Graphics::Glyph::wiggle_whiskers      
Bio::Graphics::Glyph::wiggle_xyplot An xyplot plot compatible with dense "wig"data      
Bio::Graphics::Glyph::xyplot The xyplot glyph      
Bio::Graphics::Panel Generate GD images of Bio::Seq objects      
Bio::Graphics::Pictogram generate SVG output of Pictogram display for consensus motifs      
Bio::Graphics::RendererI A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI.      
Bio::Graphics::Util non-object-oriented utilities used in Bio::Graphics modules      
Bio::Graphics::Wiggle Binary storage for dense genomic features     1.0
Bio::Graphics::Wiggle::Loader      

Documentation

feature_draw.pl Render a Bio::Graphics Feature File  
frend.pl Render a Bio::Graphics Feature File on the web  
search_overview Render a SearchIO parser report into a simple overview graphic  

Other Files

README.bioperl